tbuckley/cabot-search huggingface dataset:
OUTC-07. ANALYZING PREDICTORS OF LOSS TO FOLLOW-UP AS SEEN AMONG YOUNG SURVIVORS OF CENTRAL NERVOUS SYSTEM TUMORS FOR QUALITY IMPROVEMENT INTERVENTIONS AT DANA FARBER CANCER INSTITUTE
Authors: Tabitha Cooney, Mary Tabatneck, Amelia Stone
Journal: Neuro-Oncology (2023)

Abstract At Dana Farber Cancer Institute, children and young adults who have completed treatment for central nervous system tumors visit the Pediatric Neuro-Oncology Outcomes Clinic (“Empower”) for survivorship visits. By attending these long-term clinic visits, survivors can receive multidisciplinary services and undergo monitoring for disease recurrence. We used descriptive statistics and chi-square tests to investigate the relationship between loss to follow-up and sociodemographic factors among Empower patients. We reviewed medical records to gather data on 200 patients who had visited the clinic between 1-1-2015 and 1-1-2020, extracting information about sex, zip code, diagnosis, treatment received, and insurance type (private vs. public). We then indicated whether each patient had been “lost to follow-up,” defined as not returning to the clinic for &amp;gt;1,000 days after the recommended follow-up date. Among the 200 patients reviewed, 46 (23%) were lost to follow-up and 154 (77%) were not lost to follow-up. With respect to race and ethnicity, individuals identifying as Black, Asian, Middle Eastern, Native Hawaiian or Pacific Islander, Hispanic or Latino, or “Other” were more likely to be lost to follow-up than patients who exclusively identified as White (21% versus 39%; p=0.036). Additionally, individuals who were lost to follow-up were more likely to have been treated for low-grade gliomas as opposed to other CNS tumors (30% versus 13.6%; p=.015). Sex, the use of chemotherapy and radiation, and insurance type did not have a significant association with loss to follow-up. An analysis of the relationship between median household income and loss to follow-up is pending. The results imply that there is a significant association between non-white race, Hispanic or Latino ethnicity, a diagnosis of low-grade glioma, and loss to follow-up. The continuation of this study can provide the groundwork for interventions targeted at supporting patients who are at an increased risk of loss to follow-up.
HGG-16. COMPARATIVE ANALYSIS OF AUTOPHAGY IN DRUG RESPONSES AND AGGRESSIVE BEHAVIOR OF ADULT VERSUS PEDIATRIC GLIOMA CELL LINES
Authors: Irem Yenidogan, Nesibe Peker, Gamze Deveci, Bera Aygun, Dondu Kirmizi, Nathalie Al, Fikret Asarcikli, Banu Oflaz Sozmen, Goktug Akyoldas, Ibrahim Kulac, Ihsan Solaroglu, Devrim Gozuacik
Journal: Neuro-Oncology (2023)

Abstract Central nervous system tumors are the most common solid cancer and a leading cause of cancer-related deaths in children. Glioma is the most challenging pediatric CNS tumor with therapy resistance and poor prognosis in pediatric patients. Although histopathological analyses revealed similarities with adult brain glioma, emerging evidence suggests that the deregulated molecular pathways in pediatric glioma (p-GM) are different from that of adults. Autophagy, a cellular clearance system and a drug resistance mechanism, has been implicated in glioma progression, invasion, and relapse, yet its role in pediatric patients is not well documented. In this study, we compared the autophagic capacity of adult versus p-GM cell lines and evaluated the effect of autophagy manipulation on drug responses. In addition, migration, extracellular matrix invasion ability, and the metabolism of pediatric and adult gliomas were compared and the contribution of autophagy to the aggressive phenotype was evaluated.
CNSC-03. EXPLORING STRUCTURAL DISRUPTION OF TRICELLULAR JUNCTIONS TO ENHANCE BLOOD-BRAIN-BARRIER PERMEABILITY
Authors: Melissa Cesaire, Mahalia Dalmage, Sanghee Lim, Kwak Minhye, Kayen Tang, Christina Conrad, Baktiar Karim, Donna Butcher, Sadhana Jackson
Journal: Neuro-Oncology (2023)

Abstract The blood-brain barrier (BBB) hinders CNS chemotherapy entry for malignant glioma treatment. It is predominantly composed of brain endothelium linked by bicellular (BJ) and tricellular (TJ) tight junctions. Previous studies demonstrated,angubindin-1 inhibited TJ angulin-1 to increase brain and CSF targeted therapy in rodent lung cancer models. We hypothesize angubindin-1 can transiently decrease BBB junctional integrity to increase chemotherapy permeability and prolong rodent glioma model survival. Rat brain endothelial cells were treated with TJ and BJ inhibitors against angulin-1 (angubindin-1 600µg/mL), claudin-3 (C-CPE 200µg/mL) or claudin-5 (C-CPE-MT 200µg/mL). Endothelial integrity was assessed by immunoblotting and cell-cell electrical impedance. Effects of angubindin-1 on efflux transporter P-glycoprotein (PGP) and migration were studied using rat and human derived glioma cells. Rat glioma models were treated with doxil (3 mg/kg), angubindin-1 (10 mg/kg or 30 mg/kg), or combination therapy for assessments on tumor volume, BBB permeability and survival. We observed decreased angulin-1 expression 5 hours after angubindin-1 treatment, with return to baseline by 24 hours (p&amp;lt;0.05). Angubindin-1, CCPE, and CCPE-mt globally reduced endothelial cell-cell integrity, maximally at 4 hours with a return to baseline by 12 hours; with angubindin-1 demonstrating the largest decreased cell-adhesion (angubindin-1 vs control, p&amp;lt; 0.0001). Angubindin-1 also decreased PGP efflux of rhodamine in both endothelial and glioma cells, along with demonstrating a pro-migratory dose-dependent effect on rat glioma cells. Combined angubindin-1 and doxil increased survival in rat glioma models compared with doxil alone (24 days vs. 18 days, p &amp;lt; 0.0001). Day 14 tumor volume was significantly decreased with angubindin-1 and combination treatment respectively (77.5 % vs 81.6 %, p&amp;lt;0.05). Ongoing studies are exploring, angubindin-1’s effect on large CNS drug permeability, TJ localization post BBB disruption and additional combinational treatments in glioma models. Collectively, these findings pose a unique opportunity to disrupt BBB integrity and improve malignant glioma treatment options.
MDB-30. IDENTIFICATION AND CHARACTERIZATION OF NOVEL TRANSCRIBED ULTRACONSERVED REGIONS AS LONG NON-CODING RNAS IN MEDULLOBLASTOMA
Authors: Kadie Hudson, Myron K Gibert Jr., Ying Zhang, Collin Dube, Shekhar Saha, Ashley Vernon, Roger Abounader
Journal: Neuro-Oncology (2023)

Abstract Medulloblastoma is the most common pediatric brain tumor. While the 5-year survival rate for medulloblastoma patients has improved with molecular subgrouping, children who undergo standard of care treatments frequently experience permanent neurological deficits. Additionally, under-characterized medulloblastoma subgroups lack targeted therapies, correlating to lower survival rates for these patients. To find new therapies, a better understanding of the molecular basis of medulloblastoma is needed. This work investigates the role of “Transcribed Ultra-Conserved Regions” (TUCRs) in medulloblastoma about which there is no published literature. TUCRs represent a distinct group of 481 putative lncRNAs that are 100% conserved across human, mouse, and rat genomes. These ultra-conserved elements change 20 times slower than the average genomic region and are therefore under intense negative selection within multiple species. Since their discovery, TUCRs have only been correlated to a handful of cancers and remain exceedingly underexamined within cancer research. Using RNA-sequencing and differential gene expression analysis of medulloblastoma tumors as compared to normal human cerebellum samples, we identified a multitude of differentially expressed TUCRs spanning across all TUCR genomic annotations. In vitro experimentation using several medulloblastoma established cell lines indicated significant upregulation of these TUCR transcripts. We are currently investigating the functional effects and mechanisms of action of select differentially expressed TUCRs in medulloblastoma. Altogether, our work is investigating the oncogenic and tumor suppressive nature of TUCRs. It represents the first study of TUCRs in medulloblastoma that will significantly advance our basic understanding of this highly understudied class of molecules.
MDB-20. IMPROVING THE PERSISTENCE OF CAR T CELLS AGAINST GROUP 3 MEDULLOBLASTOMAS VIA EPIGENETIC REGULATION OF EXHAUSTION
Authors: Meghan Dukes, Haley Houke, Frederique Zindy, Ben Youngblood, Martine Roussel, Giedre Krenciute
Journal: Neuro-Oncology (2023)

Abstract Medulloblastomas (MB) are the most common malignant pediatric brain tumor with molecular subclass Group 3 (G3) requiring the most intense treatment regimen including surgery, intensive radiation followed by chemotherapy. Despite an overall 40% survival rate, survivors’ quality of life is often impaired due to whole-brain radiation leading to neurocognitive defects. Chimeric antigen receptor (CAR) T cell therapy has emerged clinically as a safe, tumor-targeted immunotherapy with the most success observed against hematological malignancies. Translating CAR T cell therapy to brain tumors has proven challenging due to lack of targetable antigens on the surface of tumor cells and lack of persistence of CAR T cells. We have previously identified that patient samples and PDOX-derived cell lines of G3 MBs consistently over-express B7-H3 (CD267) compared to normal tissue. Herein, we investigated B7-H3 targeted CAR T cell products against G3 MB in vitro and in vivo. Initial results show that B7-H3 CAR T cells are highly effective in clearing human MB tumors in NSG mice, however, 4 out 5 mice experienced late relapses that showed reduced, but still present, B7-H3 antigen expression. We hypothesize that the lack of CAR T cell persistence is ultimately responsible for tumor regrowth. To overcome this limitation, we have identified epigenetic regulators DNMT3A and TET2 that control T cell exhaustion. Using CRISPR/Cas9, we genetically knocked out DNMT3A and TET2 in CAR T cells and investigated the impact on persistence and anti-tumor activity. Our data supports the hypothesis that knock out of DNMT3A and TET2 improves antigen-dependent proliferation and persistence of B7-H3 CAR T cells against G3 MB tumor lines in vitro. DNMT3A KO shows a more sustained effect over TET2. Currently, we are optimizing in vivo experiments to investigate prolonged tumor clearance in both immunocompromised and fully immunocompetent murine models.
ATRT-06. ETMR TUMORIGENESIS MIRRORS RADIAL GLIAL DEVELOPMENT
Authors: Fupan Yao, Iqra Mumal, Nikhil Raghuram, Liming Xu, Laurie Liu, Ben Ho, Annie Huang
Journal: Neuro-Oncology (2023)

Abstract Embryonal tumors with multilayered rosettes (ETMRs) are rare pediatric brain tumors defined primarily by overexpression of the C19MC microRNA cluster. These tumors affect mostly children under the age of 3. However, little is known about the origin and developmental contexts of ETMRs. We hypothesized that the early onset of these tumors suggests an embryonic tumorigenic event. To elucidate the embryonic contexts of which ETMRs arise, we curated three mouse embryogenesis datasets representing the full spectrum of murine embryonic development. We generated timepoint structure signatures of this atlas and projected them onto a single nuclei RNA sequencing dataset of 8 primary ETMRs. Consistent with existing literature, we discovered that ETMRs resemble a spectrum of radial glial, neuronal, and oligodendrocytic cell types. We also recapitulated potential ETMR driver mechanisms such as overexpression of WNT and SHH signaling by gene set enrichment analysis. We validated the enrichment of lineage and driver markers through GSEA and marker gene enrichment in a separate cohort of ETMRs characterized by bulk RNA sequencing. Taken together, the embryonic context of ETMR development may play crucial roles in the early identification and treatments of this lethal disease.
IMMU-17. DEVELOPMENT OF AN INTRACRANIAL CANNULA IMPLANTATION SYSTEM FOR SERIAL LOCOREGIONAL CAR T CELL INFUSIONS IN MICE
Authors: Kyra Harvey, Peter Madsen, Tiffany Smith, Crystal Griffin, Luke Patterson, Nicholas Vitanza, Phillip Storm, Adam Resnick, Jessica Foster
Journal: Neuro-Oncology (2023)

Abstract Pediatric CNS tumors are responsible for the majority of cancer-related deaths in children. As many tumors lack efficacious treatments, there is a crucial need to develop more promising therapeutic options, such as immunotherapies. Of particular interest is the use of chimeric antigen receptor (CAR) T cell therapy. Current clinical trials are ongoing targeting the cell surface molecules HER2, EGFR, B7-H3, IL13RA2, and the disialoganglioside GD2. While the majority of trials deliver CAR T cells into the cerebral spinal fluid with repeated doses, this has not been completed in preclinical models due to difficulty performing multiple stereotactic surgeries. To evaluate repeated locoregional delivery of CAR T cells in preclinical murine models, we established an indwelling catheter system that recapitulates indwelling catheters currently being used in human clinical trials. Following orthotopic injection and engraftment of tumor cells in mice, intratumoral placement of a fixed guide cannula is completed on a stereotactic apparatus and secured with screws and acrylic resin. Treatment cannulas are then inserted through the fixed guide cannula for repeated CAR T cell delivery. With this system, we tested novel CAR T cells directed against glypican 2 (GPC2), resulting in significant tumor regression in medulloblastoma model 7316-4509 (p&amp;lt;0.01), as well as significantly prolonged survival in thalamic diffuse midline glioma 7316-3058 (p&amp;lt;0.05). Stereotactic placement of the guide cannula can be adjusted to deliver CAR T cells directly into the lateral ventricle or other locations in the brain. This platform offers a reliable mechanism for preclinical testing of repeated intracranial infusions of CAR T cells and other novel therapeutics, offering a superior preclinical model for translation to clinical trials.
OTHR-06. NARRATIVE MEDICINE AND THE PRACTICE OF PEDIATRIC NEURO-ONCOLOGY: GRAPPLING WITH THE UNTHINKABLE
Authors: Kathy Riley, Alison Toback
Journal: Neuro-Oncology (2023)

Abstract As pediatric neuro-oncology team members work with patients, they engage in life and death struggles on behalf of children. Among patients who survive, many are left with intellectual decline, psychological difficulties, inability to take on daily life skills, and an overall decrease in health-related quality of life (Castellino et al., 2014). Absorbing the weight of these stories of illness and complex survival leads to risk of burnout and moral distress. This research sought to understand how pediatric neuro-oncology team members at a U.S. hospital interact with, interpret, and make meaning of the illnesses, complex recoveries, and deaths of patients as a result of participating in a series of narrative medicine workshops. In the workshops, team members encountered fictional stories of loss and longing for restoration as they engaged in close reading and discussion of a text. Writing about the text after participating in discussion helped members connect more deeply to their own formative stories. Further, it enlarged their capacity to connect to the stories of fellow team members and the narratives of patients and their families. Those who practice narrative medicine seek “to recognize, absorb, interpret, and be moved to action by the stories of others” (Charon et al., 2017, p. 1). Its methods harness creativity and insight to equip those in healthcare not only to diagnose and treat their patients but to bear witness to what patients undergo (Charon et al., 2017). If team members train themselves to see the beauty, pain, complexity, and ambiguity in a work of art, they may in turn see their patients and one another as works of art. The act of engaging in narrative medicine practice as a healthcare team in and of itself alleviates distress and fosters collaborative relationships among team members as they grapple with unthinkable loss in their work.
IMMU-07. TACEDINALINE (CI994), A CLASS I HDAC INHIBITOR, TARGETS INTRINSIC TUMOR GROWTH AND LEPTOMENINGEAL DISSEMINATION IN MYC-DRIVEN MEDULLOBLASTOMA WHILE MAKING THEM SUSCEPTIBLE TO ANTI-CD47 INDUCED MACROPHAGE PHAGOCYTOSIS VIA NF-KB-TGM2 DRIVEN TUMOR INFLAMMATION
Authors: Viktoria Marquardt, Johanna Theruvath, Nan Qin, Daniel Picard, Rajeev Vibhakar, Sujatha Venkararaman, Marc Remke, Siddhartha Mitra
Journal: Neuro-Oncology (2023)

Abstract BACKGROUND While major advances have been made in improving the quality of life and survival of children with most forms of medulloblastoma (MB), those with MYC-driven tumors (Grp3-MB) still suffer significant morbidity and mortality. Here, we report a cross-entity, epigenetic drug screen to evaluate therapeutic vulnerabilities in MYC amplified medulloblastoma, which sensitizes them to macrophage-mediated phagocytosis upon targeting the CD47-SIRPa innate checkpoint pathway. METHODS We performed a primary screen including 78 epigenetic inhibitors and a secondary screen including 20 histone deacetylase inhibitors (HDACi) to compare response profiles in atypical teratoid/rhabdoid tumor (AT/RT, n=11), medulloblastoma (n=14), and glioblastoma (n=14). This unbiased approach revealed the preferential activity of HDACi in MYC-driven medulloblastoma. Importantly, the class I selective HDACi, CI-994, showed significant cell viability reduction mediated by induction of apoptosis in MYC-driven medulloblastoma, with little to no activity in non-MYC-driven medulloblastoma, AT/RT, and glioblastoma in vitro. We tested the combinatorial effect of targeting Class I HDACs and the CD47-SIRPa phagocytosis checkpoint pathway using in-vitro phagocytosis assays and in-vivo orthotopic xenograft models. RESULTS CI-994 displayed anti-tumoral effects at the primary site and the metastatic compartment in two orthotopic mouse models of MYC-driven medulloblastoma. Furthermore, RNA sequencing revealed NFκB pathway induction as a response to CI-994 treatment, followed by TGM2 expression, which enhanced inflammatory cytokine secretion. We further show interferon-gamma (IFN-g) release and cell surface expression of engulfment (“eat-me”) signals (such as calreticulin). Finally, combining CI-994 treatment with an anti-CD47 mAb targeting the CD47-SIRPa phagocytosis checkpoint enhanced in vitro phagocytosis and survival in tumor-bearing mice. CONCLUSION Together, these findings suggest a dynamic relationship between MYC amplification and innate immune suppression in MYC-amplified medulloblastoma and support further investigation of phagocytosis modulation as a strategy to enhance cancer immunotherapy responses.
DIPG-45. ELONGIN B REGULATES H3K27M CHROMATIN INCORPORATION TO PROMOTE MALIGNANCY IN DIFFUSE MIDLINE GLIOMA
Authors: Jamie Anastas, Adam Kebede, Alan Jiao, Claudia Mimoso, Rebecca Murdaugh, Barry Zee, Mariella Filbin, Karen Adelman, Yang Shi
Journal: Neuro-Oncology (2023)

Abstract Chromatin dysregulation is both a cause and consequence of aberrant RNA Polymerase II (Pol2) transcription in cancer. Some of the most striking examples of chromatin disruption in cancer include somatic mutations in genes encoding histone H3 (H3.3/H3.1K27M) observed in ~80% of diffuse midline glioma (DMG). H3K27M mutant histones act in a dominant manner to disrupt chromatin regulation and Pol2-dependent transcription in DMG. How H3K27M impinges on the Pol2 transcriptional machinery and whether aberrant Pol2 transcription can reciprocally induce chromatin dysregulation in DMG remain open questions. We conducted epigenome-focused CRISPR dropout screens and identified multiple regulators of Pol2 elongation, including Elongin B and C (ELOB/ELOC) as DMG genetic dependencies. Follow-up studies confirm that knockout (KO) of ELOB inhibits DMG proliferation in neurosphere culture and abrogates DMG tumorigenesis in orthotopic xenografts. Additional chromatin profiling studies reveal that ELOB binding sites are enriched in H3K27M mutant histones, suggesting that ELOB works together with H3K27M to promote malignant gene expression in DMG. Indeed, reciprocal knockout studies suggest that while ELOB chromatin binding patterns were not altered by H3K27M KO, ELOB KO significantly reduced H3K27M chromatin incorporation at thousands of genomic loci. Further RNAseq and PROseq analyses reveal that ELOB KO alters Pol2 transcription resulting in the up-regulation of genes associated with neuronal and muscle differentiation and the repression of glial stem cell genes. Together, these findings suggest that H3K27M chromatin binding patterns and aberrant gene regulation in DMG are, in part, dictated by ELOB and the Pol2 elongation machinery. Finally, analyses of patient datasets indicate that ELOB complex genes are overexpressed in high grade glioma and DMG and correlate with decreased patient survival. Collectively, these studies suggest that a functional interaction between ELOB and H3K27M mutant histones induces DMG-specific aberrations in chromatin and gene regulation to drive malignancy.
DIPG-26. CLINICAL AND GENOMIC ANALYSIS OF H3K27M-DMG LONG-TERM SURVIVORS REVEALS ENRICHMENT IN MAPK PATHWAY ALTERATIONS
Authors: Holly Roberts, Alberto Picca, Marc Sanson, Ulrich Schüller, Thiébaud Picart, François Ducray, Adam Green, Yoshiko Nakano, Dominik Sturm, Zied Abdullaev, Kenneth Aldape, Sebastian Waszak, Sriram Venneti, Drew Pratt, Carl Koschmann
Journal: Neuro-Oncology (2023)

Abstract INTRODUCTION H3K27M-mutant diffuse midline gliomas (H3K27M-DMGs) share a generally poor prognosis with a median overall survival (OS) of 9–12 months. However, patients with histone-mutant central nervous system (CNS) tumors and long-term survival (LTS) have been reported, in some instances beyond three years. We aim to determine characteristics of patients with H3K27M-mutant CNS tumors associated with LTS (OS&amp;gt;36 months). METHODS We performed a multi-site and literature case review of patients with confirmed H3K27M-DMG (including H3.1, H3.3, or by IHC) and LTS (OS&amp;gt;36 months) with extraction of demographic, diagnostic, molecular, therapeutic, and outcome data. We obtained a final cohort of 72 patients (median age 14 years, IQR 7-31 years). A control cohort of 453 patients with confirmed H3K27M-DMG and OS&amp;lt;18 months was created through literature review. Between the cohorts, demographic and clinical differences were compared for statistical significance (unpaired t-test and chi-squared test), excluding unknown variables, and frequent genetic alterations were compared. RESULTS There was no association with H3.3 versus H3.1 when comparing LTS (15% H3.1) and control (13.6% H3.1) cohorts. Alterations in MAPK pathway genes [NF1 (n=10), FGFR1 (n=10), and BRAF (n=9)] were more frequent in the LTS cohort, with H3.3/BRAFV600E co-mutation being reported in 8/72 (11%) LTS patients and only 5/453 (1.1%) control patients. The LTS group had a greater proportion of patients with non-infiltrative (17.5%) and low-grade (26.6%) histology tumors than the control group (1.7%, p&amp;lt;0.001 and 11.4%, p=0.001, respectively). DNA methylation analysis and RNA sequencing are currently being performed for 29 LTS patients to determine molecular sub-groups within H3K27M-DMG with improved prognosis. CONCLUSIONS Our early findings in this ongoing study suggest that both histological and molecular characteristics of H3K27M-DMG influence survival. We identify enrichment of alterations in MAPK pathway-related genes in patients with LTS. These findings hold promise for further defining and classifying H3K27M-DMG to improve prognostication.